The applicability of electro-Fenton technology to remediation of wastewater contaminated by several organic pollutants such as dyes and polycyclic aromatic hydrocarbons has been evaluated using iron-enriched zeolite as heterogeneous catalyst. The electro-Fenton technology is an advanced oxidation process that is efficient for the degradation of organic pollutants, but it suffers from the high operating costs due to the need for power investment. For this reason, in this study microbial fuel cells (MFCs) were designed in order to supply electricity to electro-Fenton processes and to achieve high treatment efficiency at low cost. Initially, the effect of key parameters on the MFC power generation was evaluated. Afterwards, the degradation of Reactive Black 5 dye and phenanthrene was evaluated in an electro-Fenton reactor, containing iron-enriched zeolite as catalyst, using the electricity supplied by the MFC. Near complete dye decolourization and 78% of phenanthrene degradation were reached after 90 min and 30 h, respectively. Furthermore, preliminary reusability tests of the developed catalyst showed high degradation levels for successive cycles. The results permit concluding that the integrated system is adequate to achieve high treatment efficiency with low electrical consumption.